Database of computational tools developed by members of the International Nucleome Consortium

(See the most updated beta-version of this database at https://github.com/COSTINC/ComputationalTools)

This repository lists the computational tools developed by COST INC (https://inc-cost.eu/) members for data analysis and modeling in the context of 4D Genomics.

This summary table enumerates (non-exhaustively) the tasks performed by the different tools:

  • Hi-C generation: functions to treat Hi-C raw data to generate Hi-C matrices or to import already processed Hi-C data
  • Hi-C analysis: functions to analyze Hi-C data to infer/compare compartments, TADs, structural motifs, etc.
  • Hi-C visualization: functions to visualize Hi-C data
  • Image analysis: functions to treat and analyse images or movies from microscopy
  • Integrative 3D modeling: top-down reconstructions of 3D genome conformations from 4D genomics data
  • Biophysical modeling: bottom-up biophysical/polymer/mechanistic models to predict chromatin organization based on specified mechanisms
  • Statistical modeling: statistical/AI models to predict contacts, TAD boundaries, structural motifs, etc. based on genomics data
Hi-C generationHi-C analysisHi-C visualizationImage analysisIntegrative 3D modelingBiophysical modelingStatistical modeling
3DEpiBlockX
BinlessXX
Chrom3DX
ChromFoldX
FAN-CXXX
HiCBricksXXX
IC-FinderX
IMGRXX
NRLcalcXX
NucToolsX
TADbitXXXX
TADdynX
TADkitX
TADpoleX
TFaffinityX